Abstract Background The decreasing cost of next-generation sequencing technologies (NGS) has resulted in their increased use in research, and in the clinic. However, France and Quebec have not yet implemented nation-wide personalized medicine programs using NGS. To produce policies on the large-scale implementation of NGS, decision makers could benefit from a detailed understanding of how these technologies are currently used, their limitations, and the benefits they could bring to patients. Objectives We aimed at answering two research questions: How are patients’ NGS data currently managed in healthcare institutions in Quebec and in France? What issues do technology users identify which should be solved in order to implement clinical genomics at the national level? Method Through a multiple case study method, we analysed interviews and documentation from four teams that use whole-exome sequencing in hybrid clinical research projects focusing on cancer and rare diseases. Results Interviewees detailed numerous challenges linked with managing the complexity of the process of collecting and interpreting data in a relevant manner for patients, and described how obtaining buy-in from multiple stakeholders was necessary. Conclusion A strong political will is essential for personalized medicine to be implemented efficiently in France and Quebec.
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